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Biomedical knowledge graphs (KGs) encode rich, structured information critical for drug discovery tasks, but extracting meaningful insights from large-scale KGs remains challenging due to their complex structure. Existing biomedical subgraph retrieval methods are tailored for graph neural networks (GNNs), limiting compatibility with other paradigms, including large language models (LLMs). We introduce K-Paths, a model-agnostic retrieval framework that extracts structured, diverse, and biologically meaningful multi-hop paths from dense biomedical KGs. These paths enable prediction of unobserved drug-drug and drug-disease interactions, including those involving entities not seen during training, thus supporting inductive reasoning. K-Paths is training-free and employs a diversity-aware adaptation of Yen's algorithm to extract the K shortest loopless paths between entities in a query, prioritizing biologically relevant and relationally diverse connections. These paths serve as concise, interpretable reasoning chains that can be directly integrated with LLMs or GNNs to improve generalization, accuracy, and enable explainable inference. Experiments on benchmark datasets show that K-Paths improves zero-shot reasoning across state-of-the-art LLMs. For instance, Tx-Gemma 27B improves by 19.8 and 4.0 F1 points on interaction severity prediction and drug repurposing tasks, respectively. Llama 70B achieves gains of 8.5 and 6.2 points on the same tasks. K-Paths also boosts the training efficiency of EmerGNN, a state-of-the-art GNN, by reducing the KG size by 90% while maintaining predictive performance. Beyond efficiency, K-Paths bridges the gap between KGs and LLMs, enabling scalable and explainable LLM-augmented scientific discovery. We release our code and the retrieved paths as a benchmark for inductive reasoning.
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This content will become publicly available on April 24, 2026
Reasoning of Large Language Models over Knowledge Graphs with Super-Relations
While large language models (LLMs) have made significant progress in processing and reasoning over knowledge graphs, current methods suffer from a high non-retrieval rate. This limitation reduces the accuracy of answering questions based on these graphs. Our analysis reveals that the combination of greedy search and forward reasoning is a major contributor to this issue. To overcome these challenges, we introduce the concept of super-relations, which enables both forward and backward reasoning by summarizing and connecting various relational paths within the graph. This holistic approach not only expands the search space, but also significantly improves retrieval efficiency. In this paper, we propose the ReKnoS framework, which aims to Reason over Knowledge Graphs with Super-Relations. Our framework’s key advantages include the inclusion of multiple relation paths through super-relations, enhanced forward and backward reasoning capabilities, and increased efficiency in querying LLMs. These enhancements collectively lead to a substantial improvement in the successful retrieval rate and overall reasoning performance. We conduct extensive experiments on a variety of datasets to evaluate ReKnoS, and the results demonstrate the superior performance of ReKnoS over existing state-of-the-art baselines, with an average accuracy gain of 2.92% across nine real-world datasets.
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- PAR ID:
- 10612757
- Publisher / Repository:
- International Conference on Learning Representations
- Date Published:
- Format(s):
- Medium: X
- Location:
- Singapore
- Sponsoring Org:
- National Science Foundation
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